[gmx-users] LR coulomb interaction

[David]

On Wed, 2005-05-04 at 19:37 +0200, Michal Kolinski wrote:
> I tried to evaluate LR Coulomb interaction energy for ligand and
> protein.  My system contains
> membrane, ligand, TM protein and ions.  I did three reruns of my
> trajectory:
> 1) leaving charges on ligand, zeroing rest 
> 2) leaving charges on protein, zeroing rest 
> 3) leaving charges on protein and ligand, zeroing rest.
> Then I calculated LR Coulomb interaction energy for prot-lig (Elr_c
> (ligand-protein)):
>  
> 
> Elr_c(protein-ligand) = Elr_c(ligand-ligand) + Elr_c(ligand-protein) +
>                                       Elr_c(protein-protein) 

principle is right, but where is the membrane and solvent? You probably
need more reruns..'


>       in my case:
>  
> 3 = 1 +  Elr_c(ligand-protein) + 2
>  
>  I also included long range corrections for each of the reruns that I
> found using –rerun –debug option.  
> Is this a right way to estimate LR coulomb interaction energy between
> two molecules, my estimated energy seems wrong  13.567.
>  Please give me some comment on this.
> Thank you in advance. 
>  
>  
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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